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Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Microfluidics]

ABSTRACT: Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures.

ORGANISM(S): Homo sapiens

PROVIDER: GSE137537 | GEO | 2019/09/21

REPOSITORIES: GEO

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Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Seq-Well]

Project description:Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures.

2019-09-23 | GSE137846 | GEO

Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Microfluidics]

Project description:Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Microfluidics]

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Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration.

Project description: Not available

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Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration

Project description:Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. These retinal defects can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. Its retinas display not only photoreceptor degeneration but also issues in other cell types starting from 4 days postfertilization (dpf). To capture these initial changes, we subjected pde6c and wild-type (WT) retinas at 5 dpf to RNA sequencing (RNA-Seq) on the Illumina HiSeq 2000 platform. The sequencing analyses indicate that the RNA-Seq dataset was of high quality. We also validated the RNA-Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) of seven phototransduction genes. We found that the fold changes of these genes measured by RT-qPCR highly correlated to those measured by RNA-Seq. Therefore, our RNA-Seq dataset likely captures the molecular changes in the whole pde6c retina. This dataset will facilitate the characterization of the molecular defects in the pde6c retina at the initial stage of retinal degeneration

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Single-cell analysis reveals inflammatory interactions driving macular degeneration

Project description:Due to commonalities in pathophysiology, age-related macular degeneration represents a uniquely accessible model to investigate therapies for neurodegenerative diseases, leading us to examine whether pathways of disease progression are shared across neurodegenerative conditions. Here we use single-nucleus RNA sequencing to profile lesions from 17 retinas with age-related macular degeneration and controls. We create a machine learning pipeline based on recent advances in data geometry and topology and identify activated glial populations enriched in the early phase of disease. Examining single-cell data from Alzheimer’s disease and progressive multiple sclerosis with our pipeline, we find a similar glial activation profile enriched in the early phase of these neurodegenerative diseases. In late-stage age-related macular degeneration, we identify a microglia-to-astrocyte signaling axis mediated by interleukin-1beta which drives angiogenesis characteristic of disease pathogenesis. Thus, due to shared glial states, the retina provides a system for investigating therapeutic approaches in neurodegenerative diseases.

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Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration

Project description:Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration

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A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration [mouse_retina_scRNAseq]

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Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-09-23 | GSE137847 | GEO

Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Seq-Well]

Project description:Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Seq-Well]

| PRJNA573659 | ENA

A unified single cell atlas of the mouse retina

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2024-02-15 | GSE243413 | GEO

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